// This model generated automatically from SBML
// WARNING: Renamed variable _space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA to xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA due to JSim namespace restrictions
// WARNING: Renamed variable _space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA to xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA due to JSim namespace restrictions
// WARNING: Renamed variable _space_3_minus_Oxoadipyl_minus_CoA to xxx_space_3_minus_Oxoadipyl_minus_CoA due to JSim namespace restrictions

// unit definitions
import nsrunit;
unit conversion off;

// SBML property definitions
property sbmlRole=string;
property sbmlName=string;
property sbmlCompartment=string;

// SBML reactions
// R06942: _space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA <=> _space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA 
// R02229: Cyclohexanol => Cyclohexanone 
// R06941: _space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA <=> _space_3_minus_Oxoadipyl_minus_CoA 

math main {
  realDomain time second;
  time.min=0;
  extern time.max;
  extern time.delta;

  // variable definitions
  real default = 1 L;
  real uVol = 1 L;
  real E1_space_1_space_1_space_90 = 0 M;
  real E4_space_2_space_1_space_17 = 0 M;
  real E1_space_1_space_1_space_35 = 0 M;
  real Cyclohexanol(time) M;
  real Cyclohexanone(time) M;
  real xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA(time) M;
  real xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA(time) M;
  real xxx_space_3_minus_Oxoadipyl_minus_CoA(time) M;
  real R06942(time) katal;
  extern real R06942.kf;
  extern real R06942.kb;
  real R02229(time) katal;
  extern real R02229.kf;
  extern real R02229.kb;
  real R06941(time) katal;
  extern real R06941.kf;
  extern real R06941.kb;

  // equations
  when (time=time.min) Cyclohexanol = 0;
  (Cyclohexanol*uVol):time = -1*R02229;
  when (time=time.min) Cyclohexanone = 0;
  (Cyclohexanone*uVol):time = R02229;
  when (time=time.min) xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA = 0;
  (xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA*uVol):time = -1*R06942;
  when (time=time.min) xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA = 0;
  (xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA*uVol):time = R06942 + -1*R06941;
  when (time=time.min) xxx_space_3_minus_Oxoadipyl_minus_CoA = 0;
  (xxx_space_3_minus_Oxoadipyl_minus_CoA*uVol):time = R06941;
  R06942 = R06942.kf*_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA - R06942.kb*_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA;
  R02229 = R02229.kf*Cyclohexanol - R02229.kb*Cyclohexanone;
  R06941 = R06941.kf*_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA - R06941.kb*_space_3_minus_Oxoadipyl_minus_CoA;

  // variable properties
  default.sbmlRole="compartment";
  uVol.sbmlRole="compartment";
  E1_space_1_space_1_space_90.sbmlRole="species";
  E1_space_1_space_1_space_90.sbmlCompartment="uVol";
  E4_space_2_space_1_space_17.sbmlRole="species";
  E4_space_2_space_1_space_17.sbmlCompartment="uVol";
  E1_space_1_space_1_space_35.sbmlRole="species";
  E1_space_1_space_1_space_35.sbmlCompartment="uVol";
  Cyclohexanol.sbmlRole="species";
  Cyclohexanol.sbmlCompartment="uVol";
  Cyclohexanone.sbmlRole="species";
  Cyclohexanone.sbmlCompartment="uVol";
  xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA.sbmlRole="species";
  xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA.sbmlName="_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA";
  xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA.sbmlCompartment="uVol";
  xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA.sbmlRole="species";
  xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA.sbmlName="_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA";
  xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA.sbmlCompartment="uVol";
  xxx_space_3_minus_Oxoadipyl_minus_CoA.sbmlRole="species";
  xxx_space_3_minus_Oxoadipyl_minus_CoA.sbmlName="_space_3_minus_Oxoadipyl_minus_CoA";
  xxx_space_3_minus_Oxoadipyl_minus_CoA.sbmlCompartment="uVol";
  R06942.sbmlRole="rate";
  R06942.kf.sbmlRole="rate";
  R06942.kb.sbmlRole="rate";
  R02229.sbmlRole="rate";
  R02229.kf.sbmlRole="rate";
  R02229.kb.sbmlRole="rate";
  R06941.sbmlRole="rate";
  R06941.kf.sbmlRole="rate";
  R06941.kb.sbmlRole="rate";
}